Fruit body rot and calyx rot caused by Alternaria alternata f. sp. mali has recently become a severe disease of Pink Lady apple in Israel. Severe fruit rot caused by A. alternata f. sp. mali has not been reported elsewhere in the world, and control measures are not currently known. Our objective was to determine the peak periods of susceptibility and develop methods to manage the disease by timing fungicide applications according to fruit phenological stage. We determined the relationship between fruit phenological stage and rot susceptibility by (i) monitoring the appearance of first fruit symptoms in the orchard; (ii) inoculating detached and attached fruit in the laboratory and orchard, respectively, at various time intervals after petal fall; and (iii) starting fungicide applications at various time intervals after petal fall. Fruit of Pink Lady acquired susceptibility to the disease at about 115 days after petal fall (DAPF) when reaching a diameter of ≥55 mm. Based on these findings, a new spray strategy was adopted involving a limited number of 4 to 6 foliar sprays of azoxystrobin + difenoconazole or tebuconazole + captan, or their alternation, starting at 115 DAPF. This strategy provided excellent control of both body rot and calyx rot in Pink Lady apple fruit in Israel.